docker-less shiny prep

runs/shiny_prep/run.cwl

 #!/usr/bin/env cwl-runner
+
 cwlVersion: v1.2
-class: Workflow
+class: CommandLineTool
+
 inputs:
-  out_folder:
-    type: string
-  in_kallisto_df:
-    type: File
+- id: r_script
+  type: File
+  inputBinding:
+    position: 0
+- id: out_folder
+  type: string
+  inputBinding:
+    position: 1
+- id: in_kallisto_df
+  type: File
+  inputBinding:
+    position: 2
+
 outputs:
-  out_dir:
-    type:
-      type: array
-      items: Directory
-    outputSource: shiny_prep/outdir
-steps:
-  shiny_prep:
-    run: ../../workflows/shiny_prep/workflow.cwl
-    in:
-      in_kallisto_df: in_kallisto_df
-      out_folder: out_folder
-    out: [outdir]
+- id: outdir
+  type:
+    type: array
+    items: Directory
+  outputBinding:
+    glob: $(runtime.outdir)/$(inputs.out_folder)
+
+baseCommand:
+- Rscript

runs/shiny_prep/run.yml

 cores: 1
-in_kallisto_df:
+r_script:
   class: File
-  path: ../kallisto_collect/kallisto_df.csv
-out_folder: out
+  path: ../../workflows/shiny_prep/shiny_prep.R
+in_kallisto_df: 
+  class: File
+  path: ../kallisto_collect/out/kallisto_df.csv
+out_folder: out
\ No newline at end of file

workflows/shiny_prep/shiny_prep.R

 #!/usr/bin/env Rscript
 
-################################################
-#### CWL-independent tests
-################################################
-
-# arc_root <- "~/gitlab_dataplant/samplearc_rnaseq_adrian/"
-# out_folder <- "runs/shiny_prep"
-# in_kallisto_df <- "runs/kallisto_collect/kallisto_df.csv"
-
-################################################
-#### Load required library
-################################################
-
-
-
 ################################################
 #### Read arguments from CLI
 ################################################

workflows/shiny_prep/workflow.cwl

-#!/usr/bin/env cwl-runner
-cwlVersion: v1.2
-class: CommandLineTool
-hints:
-  DockerRequirement:
-    dockerPull: zimmera95/rnaseq:latest
-requirements:
-  - class: InitialWorkDirRequirement
-    listing:
-      - class: File
-        location: shiny_prep.R
-baseCommand:
-- Rscript
-arguments:
-  - position: 0
-    valueFrom: shiny_prep.R
-inputs:
-- id: out_folder
-  type: string
-  inputBinding:
-    position: 1
-- id: in_kallisto_df
-  type: File
-  inputBinding:
-    position: 2
-outputs:
-- id: outdir
-  type:
-    type: array
-    items: Directory
-  outputBinding:
-    glob: $(runtime.outdir)/$(inputs.out_folder)